The quality and quantity of DNA samples for genetic analysis is critical, e.g. Report of Working Group on Biomedical Technology, “Recommendation for a Human Cancer Genome Project,” (February, 2005). A variety of techniques have been developed for amplifying scarce DNA samples, but each involve technical trade-offs so that none is optimal in every circumstance, e.g. Hawkins et al, Current Opinion in Biotechnology, 13: 65-67 (2002); Dean et al, Proc. Natl. Acad. Sci., 99: 5261-5266 (2002). For example, many new DNA sequencing technologies provide tremendous throughput based on short sequence reads, which limits their application to the analysis of relatively small genomes, such as viral and prokaryotic genomes, e.g. Margulies et al, Nature, 437: 376-380 (2005); Shendure et al, Science, 309: 1728-1732 (2005). Many important problems related to mammalian-sized genomes could be amenable to analysis by such technologies, e.g. analysis of cancer genes, if there were available techniques to selectively amplify subsets of large genomes without biases or other deficiencies associated with common amplification techniques.